The LL fans come with a Lighting Node Pro (LNP). The 3 packs also come with an RGB Fan Controller that will control up to 6 fans (RGB only). So ... you can purchase one 3 pack and then 3 individual fans.
Your lighting expansion kit could also be controlled by the same LNP that comes with your fans ... one RGB control port would connect to the fan RGB controller and the other would connect to your strip.
The Commander Pro, btw, DOES control lighting ... it will act, essentially, as another LNP as it has 2 RGB LED ports. That said, you will still need the RGB Fan Controller hub. So ... you could absolutely use the Commander Pro in lieu of the LNP that comes with your 3 pack of fans. You'd then have 1 spare LNP.
If your motherboard has 4 pin fan headers, you won't need the C-Pro for PWM control. Most current motherboards do have 4 pin headers but I'm not sure if that micro board that you have would have a header for every fan that you want to control.